Hi Alex,
I was looking as well for a ‘cheaper’ way to build an AT, than using a much more expensive pixhawk and found the same article from Patrick Duffy (all credits to him). The idea using an Aduino board was exactly what I had in mind. As Patrick wrote, the servo shield for an Arduino Uno is optional, but very useful. A good point to start is the sample sketch on Patrick’s blog.
Getting MP to talk to the Arduino is pretty simple (hope this is the answer you are looking for). As soon as you connect the Arduino via USB cable to you PC you will have to check in the Windows device manager for the assigned COM port and select this one one the MP>Optional Hardware>AntennaTracker screen. As interface you select the ArduTracker, COM port the one taken from the device manager, 57600 bps and the ‘Connect’ button. If you have whatever software to monitor the traffic between both, you will see constantly the pan/tilt strings transmitted to the Arduino. I was under the impression, that a GPS connected to the PC you are using is required (and I’m still looking around to do so), but as soon as you set on the MP ‘Flight Plan’ screen’ the tracker position (right click and select Tracker Home), the servos for pan and tilt connected to the Arduino board should start moving. To test the setup I placed the my laptop with the attached Arduino in my car on the way home from work, with the ‘Tracker Home’ set to my home location. As closer you get as more movement on the servos you can actually notice. Hope this answers your question.
If you use the servo shield - I noticed some difference in the pin numbering in my case. Maybe there are some different versions out there, but you can try plugging the servos in the available ports or change the pin numbers in the sketch. The Arduino sketch from Patricks blog has an instruction (line 151) to receive the ‘tilt delay’ value from the MP screen, but I could never get to the point to actually see this string coming from MP (tried at the serial connect, changing the value e.g.). As well the values for ‘speed’ and ‘acceleration’ are in the MP source code (maybe for future builds), but are not transmitted to the Arduino. They are actually greyed out when you select the ArduTracker, but are available if you choose the Maestro board.
I’m pretty new to MP, drones e.g., so this is the reason I’m looking myself for someone that has more experience and has maybe a way to use the Laptop GPS as reference instead of the Tracker Home pin.
Anyway, if I could help in something, would be great. If you have any other question, please feel free to reply.

Thank you so much Peter,
That’s exactly the answer to my question. As soon as I am back home from the US I will apply your information. For now I am happy cruising in the Caribean.
I hope to contact you soon again.

Great! You are very welcome! I’m happy I could finally be helpful for someone else, instead of always needing help from others.
Hope you enjoy your cruise in the Caribbean! So you are actually very close. I’m living for 15 years in Puerto Rico.